Model of the cerebellar granular network (Sudhakar et al 2017)

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Accession:232023
"The granular layer, which mainly consists of granule and Golgi cells, is the first stage of the cerebellar cortex and processes spatiotemporal information transmitted by mossy fiber inputs with a wide variety of firing patterns. To study its dynamics at multiple time scales in response to inputs approximating real spatiotemporal patterns, we constructed a large-scale 3D network model of the granular layer. ..."
Reference:
1 . Sudhakar SK, Hong S, Raikov I, Publio R, Lang C, Close T, Guo D, Negrello M, De Schutter E (2017) Spatiotemporal network coding of physiological mossy fiber inputs by the cerebellar granular layer. PLoS Comput Biol 13:e1005754 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Cerebellum;
Cell Type(s): Cerebellum golgi cell;
Channel(s): I A; I Calcium; I K; I K,Ca; I Na,t; I h; I Na,p; I T low threshold;
Gap Junctions: Gap junctions;
Receptor(s): AMPA; NMDA; Gaba;
Gene(s):
Transmitter(s): Glutamate; Gaba;
Simulation Environment: NEURON;
Model Concept(s): Spatio-temporal Activity Patterns; Oscillations; Synchronization; Winner-take-all;
Implementer(s): Hong, Sungho [shhong at oist.jp]; Guo, Daqing [dqguo at uestc.edu.cn]; Raikov, Ivan [ivan.g.raikov at gmail.com]; Publio, Rodrigo [publio at oist.jp]; De Schutter, Erik [erik at oist.jp];
Search NeuronDB for information about:  AMPA; NMDA; Gaba; I Na,p; I Na,t; I T low threshold; I A; I K; I h; I K,Ca; I Calcium; Gaba; Glutamate;
// vecevent.ses
//
// Written by Shyam Kumar Sudhakar, Ivan Raikov, Tom Close, Rodrigo Publio, Daqing Guo, and Sungho Hong
// Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Japan
// Supervisor: Erik De Schutter
//
// Correspondence: Sungho Hong (shhong@oist.jp)
//
// September 16, 2017

load_file("nrngui.hoc")
objectvar save_window_, rvp_
objectvar scene_vector_[4]
objectvar ocbox_, ocbox_list_, scene_, scene_list_
{ocbox_list_ = new List()  scene_list_ = new List()}
{pwman_place(0,0,0)}

//Begin ArtCellGUI[0]
{
load_file("netbild.hoc")
}
ocbox_ = new ArtCellGUI(1)
{object_push(ocbox_)}
{
tobj = new MechanismStandard("VecStim")
}
{append(tobj, "vs")}
{object_pop()}
{
ocbox_.map("ArtCellGUI[0]", 397, 26, 449.28, 291.84)
}
objref ocbox_
//End ArtCellGUI[0]


//Begin NetGUI[0]
{
load_file("netbild.hoc")
}
{ocbox_ = new NetGUI(1)}
{object_push(ocbox_)}
{mapold2new = new Vector()  missing = new List()}
original_type("vs")
newnode(0, -23, 27)
{create_ = 1  create1()}
{g.size(-166.667,166.667,-125.277,125.277)}
{object_pop()}
{
ocbox_.map("NetGUI[0]", 334, 390, 527.04, 327.36)
}
objref ocbox_
//End NetGUI[0]


//Begin SpikePlot[0] for NetData[0]
{
load_file("netbild.hoc")
}
{ocbox_ = new SpikePlot(NetData[0],1)}
{object_push(ocbox_)}
mode = 1
fwindow = 100
binwidth = 0.1
build()
{g.size(0,150,0,2)}
{object_pop()}
{
ocbox_.map("SpikePlot[0] for NetData[0]", 893, 30, 304.32, 333.12)
}
objref ocbox_
//End SpikePlot[0] for NetData[0]

{
xpanel("RunControl", 0)
v_init = -65
xvalue("Init","v_init", 1,"stdinit()", 1, 1 )
xbutton("Init & Run","run()")
xbutton("Stop","stoprun=1")
runStopAt = 5
xvalue("Continue til","runStopAt", 1,"{continuerun(runStopAt) stoprun=1}", 1, 1 )
runStopIn = 1
xvalue("Continue for","runStopIn", 1,"{continuerun(t + runStopIn) stoprun=1}", 1, 1 )
xbutton("Single Step","steprun()")
t = 3813.58
xvalue("t","t", 2 )
tstop = 150
xvalue("Tstop","tstop", 1,"tstop_changed()", 0, 1 )
dt = 0.025
xvalue("dt","dt", 1,"setdt()", 0, 1 )
steps_per_ms = 40
xvalue("Points plotted/ms","steps_per_ms", 1,"setdt()", 0, 1 )
xcheckbox("Quiet",&stdrun_quiet,"")
realtime = 0
xvalue("Real Time","realtime", 0,"", 0, 1 )
xpanel(16,105)
}

//Begin VariableTimeStep
{
ocbox_ = NumericalMethodPanel[0]
ocbox_ = ocbox_.b1
ocbox_.map("VariableTimeStep", 6, 504, 272.64, 106.56)
}
objref ocbox_
//End VariableTimeStep

objectvar scene_vector_[1]
{doNotify()}

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